ACLOCAL_AMFLAGS=-I m4

SUBDIRS=$(subdirs)
DIST_SUBDIRS=$(subdirs)

AM_CXXFLAGS=-DDATAPATH='"$(datadir)/mapseq"' # -I$(srcdir)/eutils

mapseqref_files= # data/mapseqref.fasta.ltps119tax data/mapseqref.fasta data/mapseqref.fasta.mscluster data/mapseqref.fasta.ncbitax data/mapseqref.fasta.otutax data/mapseqref.gold.fasta data/mapseqref.gold.fasta.tax

#noinst_LIBRARIES=libmapseqali.a
#libmapseqali_a_SOURCES=eseqali.h eseqali.cpp eseq.h eseq.cpp

#dist_man_MANS=man/mapseq.1


bin_PROGRAMS=mapclust
#noinst_bin_PROGRAMS=kmerseqtables
#bin_SCRIPTS=tree-convert-json.esh

#LIBS=`eutils-config --libs || eutils/eutils-config --libs`
EXTRA_PROGRAMS=kmerseqtables
EXTRA_DIST=manual/mapseq-manual.tex manual/mapseq-manual.pdf data/make-transtable.sh data/prot_trans_table.h data/transl_table $(mapseqref_files)


#mapseqrefdir = $(datadir)/mapseq
#mapseqref_DATA=$(mapseqref_files)

# data/mapseqref.fa data/mapseqref.ncbitax data/mapseqref.otutax 

mapclust_SOURCES=mapclust.cpp eseqali.h ekmerhashmap.h ekmerhashmap_dec.h kmerseqtables-data.h eseqali.h eseqali.cpp eseq.h eseq.cpp
#mapseq_LDADD=libmapseqali.a eutils/libeutils.la
mapclust_LDADD=#eutils/libeutils.la
mapclust_DEPENDENCIES=kmerseqtables-data.h

kmerseqtables_SOURCES=kmerseqtables.cpp
#kmerseqtables_LDADD=eutils/libeutils.la
#kmerseqtables_DEPENDENCIES=eutils/libeutils.la

# needed to force make to make this file before making kmerfilter
#BUILT_SOURCES=kmerseqtables-data.h

#kmerseqtables-data.h : kmerseqtables
#	./kmerseqtables